README.md

In gustavdelius/mizerUR: Unstructured Resources for Mizer

mizerUR

The extension mechanism in mizer has evolved further. This package is now obsolete.

This is an extension package for the mizer package https://sizespectrum.org/mizer/. Mizer has a size-structured planktonic resource. With this extension you can also model any number of unstructured resource components. Such unstructured components are appropriate whenever the predation on these components is not size based.

Possible applications include the modelling of detritus as a resource for detritivores, carrion as a resource for scavengers, or macroflora on which fish can graze.

Installation

You can install mizerUR from GitHub with:

devtools::install_github("gustavdelius/mizerUR")

Example

The mizerUR package facilitates adding unstructured resource components to an existing MizerParams object. Here we will illustrate the process with an example MizerParams object that ships with the mizer package.

I will provide a more realistic example here once it is ready and tested.

library(mizer)
library(mizerUR)
params <- NS_params
params@species_params$species
#>  [1] "Sprat"   "Sandeel" "N.pout"  "Herring" "Dab"     "Whiting" "Sole"   
#>  [8] "Gurnard" "Plaice"  "Haddock" "Cod"     "Saithe"

Let us introduce a detritus component. The mizerUR package provides a function detritus_dynamics() that we will use to model the detritus. We set this up by creating a named list

dynamics <- list(detritus = "detritus_dynamics")

The detritus_dynamics() function uses two parameters

• detritus_external gives the rate of change of detritus from external sources in grams/year,
• detritus_proportion gives the proportion of the biomass consumed by fish that flows into the detritus component.

We need to give values for these parameters in a named list

dynamics_params <- list(`detritus_external` = 0,
                        `detritus_proportion` = 0.1)

Finally we need to specify the rate in proportion/year at which fish encounter detritus biomass. We use an allometric rate for this, which means that we only need to specify the rate for a fish of 1 gram and rates at other sizes will be scaled appropriately. This rate is species specific, so it goes into a new column in the species_params data frame. Let us set some (unrealistic made-up) values.

params@species_params$rho_detritus <- 
    c(0, 0, 0, 0, 1, 5, 10, 0, 20 ,10, 12, 5) * 1e-15

We can now add the detritus component with setUR().

params <- setUR(params, dynamics, dynamics_params)

See the help page for setUR() for more details.

The initial value of the resource biomass is URInitial(params). We set it as follows:

URInitial(params) <- c(detritus = 10^12)

We can now run the model in the usual way using the project() function of the mizer package.

sim <- project(params, progress_bar = FALSE)

We can extract the detritus biomass from the sim object with UR(sim) which will return an array with one row for each saved time in the sim object. We can use this in a plot for example.

library(ggplot2)
ggplot(melt(UR(sim))) +
    geom_line(aes(x = t, y = value)) +
    scale_y_log10() +
    xlab("Time [years]") +
    ylab("Detritus biomass [g]")

gustavdelius/mizerUR documentation built on June 24, 2020, 6:28 p.m.